If you adore the cozy flavors of autumn, you are going to love this Pumpkin Cheesecake Muffins Recipe. These muffins perfectly combine moist, spiced pumpkin batter with a luscious swirl of creamy cheesecake, creating little pockets of pure comfort in every bite. Whether you are baking for a festive brunch or a sweet afternoon treat, these muffins bring warmth, sweetness, and that irresistible fall vibe to your kitchen. Trust me, once you try this recipe, it will become a go-to favorite that you’ll find yourself making again and again.

Ingredients You’ll Need
The secret to these Pumpkin Cheesecake Muffins lies in simple, wholesome ingredients that work beautifully together to achieve the perfect texture and flavor. Each component plays its part—from the fragrant pumpkin pie spice to the silky cream cheese filling—resulting in moist, tender muffins with a delightful creamy center.
- All-purpose flour (1 3/4 cups): Provides the structure needed for tender muffins without weighing them down.
- Baking soda (1 teaspoon): Helps the muffins rise to a light and fluffy texture.
- Pumpkin pie spice (2 teaspoons): A classic blend of cinnamon, nutmeg, ginger, and cloves that brings those unmistakable fall flavors.
- Salt (1/2 teaspoon): Enhances the overall taste by balancing sweetness and spice.
- Pumpkin puree (1 cup): Adds moisture, color, and that signature pumpkin flavor.
- Eggs (2 large): Bind ingredients together and help create a rich, tender crumb.
- Brown sugar (1/2 cup): Delivers a deep, caramel-like sweetness and moist texture.
- Granulated sugar (1/4 cup plus 1/4 cup for filling): Balances sweetness and lightens texture.
- Vegetable oil (1/2 cup): Keeps the muffins moist and soft long after baking.
- Vanilla extract (1 teaspoon plus 1/2 teaspoon for filling): Adds warmth and depth to both the pumpkin batter and cheesecake filling.
- Cream cheese (8 ounces, softened, full-fat block): The star of the cheesecake swirl—smooth, tangy, and indulgent.
- Egg yolk (1 for filling): Enriches the cheesecake mixture for that silky texture.
How to Make Pumpkin Cheesecake Muffins Recipe
Step 1: Prepare the Cream Cheese Filling
Start by beating the softened cream cheese with 1/4 cup of granulated sugar, the egg yolk, and 1/2 teaspoon of vanilla extract until you get a smooth, creamy filling. This cheesecake mixture will be the luscious surprise inside each muffin, so make sure it’s silky and well combined. Set it aside as you move on to the batter.
Step 2: Mix Dry Ingredients
In a large bowl, whisk together the flour, baking soda, pumpkin pie spice, and salt. This dry mix is the backbone of your muffins, delivering that perfect balance of rise and spice with each bite.
Step 3: Combine Wet Ingredients
In another bowl, mix the pumpkin puree with brown sugar, granulated sugar, eggs, vegetable oil, and vanilla extract until the mixture is smooth and well blended. This mix brings moisture and sweetness to the muffins, making them wonderfully tender and flavorful.
Step 4: Combine Wet and Dry
Add the wet ingredients into the dry ingredients and stir gently until just combined. Be careful not to overmix here; a few lumps are okay and will help keep the muffins light and tender.
Step 5: Assemble the Muffins
Spoon about a tablespoon of the pumpkin batter into each muffing cup that you’ve either greased or lined with paper. Next, add a heaping teaspoon of the cream cheese filling right in the center. Top it with another tablespoon of pumpkin batter, then gently swirl the two batters together with a toothpick to create a beautiful marble effect. This swirling is what makes them look as fabulous as they taste!
Step 6: Bake to Perfection
Bake the muffins in a preheated oven at 350°F (175°C) for 18 to 22 minutes. You’ll know they’re ready when the pumpkin portion is set and a toothpick inserted into that part comes out clean. The cheesecake center should remain creamy but set. The kitchen will be filled with an irresistible pumpkin-spiced aroma by this point.
Step 7: Cool and Enjoy
Let the muffins cool in the pan for about 5 minutes before transferring them to a wire rack to cool completely. This short cooling time helps them release easily from the tins while keeping their moistness intact. Now your Pumpkin Cheesecake Muffins are ready to be devoured!
How to Serve Pumpkin Cheesecake Muffins Recipe
Garnishes
A light dusting of powdered sugar or a drizzle of maple glaze really elevates these muffins. You can also sprinkle chopped pecans or a pinch of cinnamon on top right after baking for a lovely crunchy contrast and extra warmth in flavor.
Side Dishes
For a complete autumn-inspired snack or breakfast, serve these muffins alongside a steaming cup of chai tea, coffee, or hot apple cider. A simple bowl of fresh fruit or a bright green salad with a citrus dressing pairs beautifully to balance the richness of the muffins.
Creative Ways to Present
Try cutting the muffins in half and spreading a little bit of butter or cream cheese frosting inside. You can also use mini muffin tins to make bite-sized versions, perfect for parties or on-the-go treats. Wrapping each muffin in parchment paper and tying with rustic twine makes a charming homemade gift, too.
Make Ahead and Storage
Storing Leftovers
Leftover Pumpkin Cheesecake Muffins can be stored in an airtight container at room temperature for up to 2 days. To keep them fresh longer, refrigerate for up to 5 days, but be sure to bring them back to room temperature or warm slightly before serving to revive their moist texture.
Freezing
These muffins freeze wonderfully! Wrap each muffin individually in plastic wrap and place them in a freezer-safe bag. They can be frozen for up to 2 months without losing flavor or texture. When ready to enjoy, thaw overnight in the refrigerator or at room temperature for a few hours.
Reheating
Warm your Pumpkin Cheesecake Muffins gently in the microwave for about 15 to 20 seconds or pop them in a 325°F oven for 5 to 7 minutes. This brings back their soft, moist quality and revives that irresistible cream cheese swirl.
FAQs
Can I use canned pumpkin puree for this recipe?
Absolutely! Canned pumpkin puree is perfect for this Pumpkin Cheesecake Muffins Recipe and provides consistent moisture and flavor. Just be sure to use pure pumpkin and not pumpkin pie filling, which contains added sugars and spices.
Is it okay to substitute the vegetable oil with butter?
You can swap vegetable oil for melted unsalted butter, but keep in mind that oil tends to keep muffins moister. Using butter will add a richer flavor but might make the texture slightly denser.
Can I make these muffins dairy-free?
To make a dairy-free version, substitute the cream cheese with a dairy-free cream cheese alternative and ensure all other ingredients like butter or milk are replaced with plant-based options. The texture and flavor may vary slightly but will still be delicious!
How do I prevent the cream cheese filling from leaking out during baking?
Use a heaping teaspoon of filling and place it in the center of the muffin batter, then gently cover with the second layer of batter. Swirling lightly with a toothpick helps the filling incorporate without spilling over. Don’t overfill the cups to avoid any leaks.
Can I add mix-ins like nuts or chocolate chips?
Definitely! Chopped walnuts, pecans, or mini chocolate chips make wonderful additions to the batter. Just fold them in gently after combining the wet and dry ingredients for extra texture and flavor twists in your Pumpkin Cheesecake Muffins Recipe.
Final Thoughts
Making these Pumpkin Cheesecake Muffins Recipe is such a joy, and sharing them feels like giving a warm, delicious hug to everyone around you. Their tender pumpkin base combined with creamy cheesecake swirls perfectly captures the essence of autumn in every bite. I encourage you to try this recipe soon—it’s an absolute crowd-pleaser that will brighten up any day or special occasion with its lovely flavor and cozy vibes.
Print
Pumpkin Cheesecake Muffins Recipe
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Total Time: 35 minutes
- Yield: 12 muffins
- Category: Dessert
- Method: Baking
- Cuisine: American
Description
Delight in these moist and flavorful Pumpkin Cheesecake Muffins, combining classic pumpkin spices with a creamy cheesecake center. Perfect for fall breakfasts or a cozy snack, these muffins feature a tender crumb and a rich cheesecake swirl that adds a touch of indulgence.
Ingredients
Dry Ingredients:
- 1 3/4 cups all-purpose flour
- 1 teaspoon baking soda
- 2 teaspoons pumpkin pie spice
- 1/2 teaspoon salt
Wet Ingredients:
- 1 cup pumpkin puree
- 2 large eggs
- 1/2 cup brown sugar
- 1/4 cup granulated sugar
- 1/2 cup vegetable oil
- 1 teaspoon vanilla extract
Cheesecake Filling:
- 8 ounces cream cheese (softened, full-fat block)
- 1/4 cup granulated sugar
- 1 egg yolk
- 1/2 teaspoon vanilla extract
Instructions
- Prepare the cheesecake filling: In a medium bowl, beat together the softened cream cheese, granulated sugar, egg yolk, and vanilla extract until the mixture is smooth and creamy. Set this aside for later use.
- Mix dry ingredients: In a large bowl, whisk together the all-purpose flour, baking soda, pumpkin pie spice, and salt evenly to create your dry base.
- Combine wet ingredients: In a separate bowl, mix the pumpkin puree, brown sugar, granulated sugar, eggs, vegetable oil, and vanilla extract until the mixture is smooth.
- Combine wet and dry ingredients: Add the wet ingredients to the dry ingredients and gently stir until just combined, ensuring not to overmix to keep the muffins tender.
- Assemble the muffins: Spoon approximately 1 tablespoon of the pumpkin batter into each greased or lined muffin cup. Add 1 heaping teaspoon of the cheesecake filling in the center, then top with another tablespoon of pumpkin batter. Swirl gently with a toothpick to create a marbled effect.
- Bake the muffins: Place the muffin tin in a preheated oven and bake at 350°F (175°C) for 18 to 22 minutes, or until the muffins are set and a toothpick inserted into the pumpkin portion comes out clean.
- Cool and serve: Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely. Enjoy warm or at room temperature.
Notes
- Do not overmix the batter to ensure muffins remain light and fluffy.
- Be sure the cream cheese is softened to mix smoothly and avoid lumps in the filling.
- Swirling the filling gently helps create a beautiful marble effect without fully blending the cheesecake into the pumpkin batter.
- Use fresh pumpkin puree for the best flavor, or canned pumpkin puree if preferred.
- These muffins can be stored in an airtight container at room temperature for up to 2 days or refrigerated for up to 5 days.
- Reheat briefly in the microwave if desired for a warm treat.

